title: Proteogenomic database construction driven from large scale RNA-seq data.
abstract: The advent of inexpensive RNA-seq technologies and other deep sequencing technologies for RNA has the promise to radically improve genomic annotation, providing information on transcribed regions and splicing events in a variety of cellular conditions. Using MS-based proteogenomics, many of these events can be confirmed directly at the protein level. However, the integration of large amounts of redundant RNA-seq data and mass spectrometry data poses a challenging problem. Our paper addresses this by construction of a compact database that contains all useful information expressed in RNA-seq reads. Applying our method to cumulative C. elegans data reduced 496.2 GB of aligned RNA-seq SAM files to 410 MB of splice graph database written in FASTA format. This corresponds to 1000× compression of data size, without loss of sensitivity. We performed a proteogenomics study using the custom data set, using a completely automated pipeline, and identified a total of 4044 novel events, including 215 novel genes, 808 novel exons, 12 alternative splicings, 618 gene-boundary corrections, 245 exon-boundary changes, 938 frame shifts, 1166 reverse strands, and 42 translated UTRs. Our results highlight the usefulness of transcript + proteomic integration for improved genome annotations.
authors.affiliation: Department of Electrical and Computing Engineering, ¶Department of Bioinformatics and Systems Biology, and §Department of Computer Science, University of California, San Diego , La Jolla, California 92093, United States.
authors.forename: Sunghee
authors.initials: S
authors.lastname: Woo
authors.forename: Seong Won
authors.initials: SW
authors.lastname: Cha
authors.forename: Gennifer
authors.initials: G
authors.lastname: Merrihew
authors.forename: Yupeng
authors.initials: Y
authors.lastname: He
authors.forename: Natalie
authors.initials: N
authors.lastname: Castellana
authors.forename: Clark
authors.initials: C
authors.lastname: Guest
authors.forename: Michael
authors.initials: M
authors.lastname: MacCoss
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001331:Automation; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D030562:Databases, Protein; D016678:Genome; D015801:Helminth Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D020543:Proteome; D017423:Sequence Analysis, RNA
chemical_list: D015801:Helminth Proteins; D020543:Proteome